You wake up with Zinnia in your arms. She still asleep. The sky is a baby blue, not a cloud in sight.
"Hroooooooooo!" Rayquaza screams coming down to sky pillar. Zinnia wakes up, startled. From the looks of it Rayquaza hasn't been battling.
"Was Deoxis up there?" You ask. Rayquaza shakes it's head. You return it to its pokeball. Over the horizon you see an unnatural storm brewing.
"Zinnia. Let's go to my house till the storm passes." You say
"Okay (y/n)." She replies.
You two get on Zinnia's Salamence and flew to Littleroot town.
Once home you introduce Zinnia to your mother."Well isn't she a cutie." Your Mother says causing Zinnia to blush.
"Sorry for intruding but (y/n) insisted that I come over and wait out the storm." Zinnia tells you Mother
"It's fine dear. I'm so happy that my baby has found love."
You take Zinnia up to you room to get away from your Mother being able to embarrass you. The two of you talk about the events of the past 3 years. She tells you that she went to many different regions and caught lots of different Pokémon. However she never stopped thinking about you and the day that you saved the world with her help. You smile at her and told her that you couldn't stop thinking about her either. Zinnia then grabs a pokeball from her belt.
"This is a Pokémon I caught from the Unova Region." She says to you as she sends the Pokémon out of it's pokeball. What comes out is a surprise.
"A Salamence? Isn't the Pokémon you wanted to show me from Unova? Salamence are native to Hoenn." You tell her
She chuckles. "Zoroark reveal yourself."
The form of the Pokémon starts to change from a blue dragon to a black fox. It leaves you in awe. You feel one of your pokeballs shaking on your belt. It's Luna's pokeball. You let her out and she goes over to Zoroark.
"Hey after the storm passes do you want to go catch some Pokemon? After the primal incident with Kyogre many new species of Pokemon have started appearing around Hoenn." You ask Zinnia
"Sure. It would be nice to spend more time with you (y/n). We have got 3 years to catch up on after all." she replies smiling at you.
Finally the storm passes. You both grab your stuff and head down stairs. You say goodbye to your Mum and leave. The first place you two go is to the battle resort.
"Wow. I didn't know this place existed." Zinnia exclaims.
You tell Zinnia everything you know about the battle resort. After you take part in some battles. You two get quite far with the powerful duo of Luna, Zinnia (your salamence) and Zinnia's Tyrantrum and Altaria.
"I've had some much fun today (Y/N). What are we doing next?" Zinnia hugs your arm.
"I don't know. What do you want to do?" You reply.
You look to the sky to see that it is mid-day. Then a black bird figure speeds past.
"What's that?" You ask.
"Hm. What's what?" Zinnia turns to you confused.
"I thought I saw something." You reply heading to the docks. It's time for Zinnia to make a more diverse team. You get a boat ride back to Petalburg city and then head up to Rustboro.
"Why are we here (Y/N)?" Zinnia turned to face you.
You give her a smile and continue leading her on to route 116. Your plan is to help her catch some new pokemon. She is really powerful with only dragon types. You can't imagine what she would be like with a team that had more coverage. In theory, Zinnia is likely to keep Salamence on her team and she has a Zoroark so that's two out of six. Suddenly it starts to rain again.
"Not another random storm." Zinnia exclaims.
You hear thunder in the sky and Zinnia jumps to grab your arm. This surprises you. So far she has shown very little that scares her. Looking around you see a cave opening.
"Let's go in here until the storm passes." You say leading her to the cave.
"It doesn't make any sense, one minute it's blazing sunlight and the next it's pouring it down." Zinnia replies.
You sit down at the entrance at watch the rain come down. Then you hear a noise from deeper in the cave. You stand. Zinnia sits still, focused on the rain.
"Looks like I wasn't the only one to take shelter in this cave." A voice echoes.
"Who are you?" You shout back.
Out of the darkness steps the former champion Steven Stone.
"Steven!" You exclaim shocked to see him " It's been a while. How have you been?""I'm fine thank you. However I'm glad I ran into you." He replies "Team Aqua and Magma are at it again and this time they've teamed up. They have gone to other regions are captured the legendary Pokémon from there."
Your face loses all emotion. Team Aqua and Magma have teamed up. Zinnia comes up from behind you and sees the look of your face.
"What's wrong (Y/N)?" She asks
"Team Aqua and Magma have teamed up. This is very bad. Steven do you know where they are?" You ask Steven
"Maybe. Multiple people have reported individuals in red and blue clothing going to the Jagged Pass."
"Then that's where we start our search." You reply.
The three of you set off for the Jagged pass in hopes to find the new base of the now combined team Aqua and Magma.
It doesn't take long before you arrive, thanks to Latias, Zinnia's Salamence and Steven's Skarmory. Searching for the base on the other hand seems impossible.
"It's going to take forever to find this base." You complain to yourself. Just then a part of the mountain crumbles away.
"Over there. Do you see it. A lever." Steve shouts.
He pulls it and another part of the mountain opens up. Inside is pitch black. You and Zinnia enter, holding hands, prepared for the worst.
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Note: I will still need suggestions on what Pokémon to include. I am only going to put Absol and Salamence in. The rest of the teams are up to you guys.Some pokemon will.make up our team, others go to Zinnia and a few other characters.Remember anything from Red and Blue to Omega Ruby and Alpha Sapphire. PS sorry for the long delay on this part. I wanted to give you lovely people a chapter worth a proper read. The next chapter will probably take a lot of time as well.Big thanks to @Silver_Hyperdeath for suggesting Zoroark as a pokemon to include in this part.